Optimization of Porous Silicon Conditions for DNA-based Biosensing via Reflectometric Interference Spectroscopy

Rahimi, Fereshteh; Fardindoost, Somayeh; Sepehri, Fatemeh; Makiyan, Farideh; Shafiekhani, Azizollah; Hossein Rezayan, Ali

doi:10.22074/cellj.2019.5598

Optimization of Porous Silicon Conditions for DNA-based Biosensing via Reflectometric Interference Spectroscopy

Document Type : Original Article

Authors

¹ Division of Nanobiotechnoloy, Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran

² Department of Physics, Sharif University of Technology, Tehran, Iran

³ 4Department of Physics, Alzahra University, Tehran, Iran ;5School of Physics, Institute for Research in Fundamental Sciences, Tehran, Iran

10.22074/cellj.2019.5598

Abstract

Objective
Substantial effort has been put into designing DNA-based biosensors, which are commonly used to detect presence of known sequences including the quantification of gene expression. Porous silicon (PSi), as a nanostructured base, has been commonly used in the fabrication of optimally transducing biosensors. Given that the function of any PSi-based biosensor is highly dependent on its nanomorphology, we systematically optimized a PSi biosensor based on reflectometric interference spectroscopy (RIS) detecting the high penetrance breast cancer susceptibility gene, BRCA1.
Materials and Methods
In this experimental study, PSi pore sizes on the PSi surface were controlled for optimum filling with DNA oligonucleotides and surface roughness was optimized for obtaining higher resolution RIS patterns. In addition, the influence of two different organic electrolyte mixtures on the formation and morphology of the pores, based on various current densities and etching times on doped p-type silicon, were examined. Moreover, we introduce two cleaning processes which can efficiently remove the undesirable outer parasitic layer created during PSi formation. Results of all the optimization steps were observed by field emission scanning electron microscopy (FE-SEM).
Results
DNA sensing reached its optimum when PSi was formed in a two-step process in the ethanol electrolyte accompanied by removal of the parasitic layer in NaOH solution. These optimal conditions, which result in pore sizes of approximately 20 nm as well as a low surface roughness, provide a considerable RIS shift upon complementary sequence hybridization, suggesting efficient detectability.
Conclusion
We demonstrate that the optimal conditions identified here makes PSi an attractive solid-phase DNA-based biosensing method and may be used to not only detect full complementary DNA sequences, but it may also be used for detecting point mutations such as single nucleotide substitutions and indels.

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